Publications
For a completely up to date list of publications see my google scholar page here.
Preprints
Williams MJ, Funnell T, O’Flanagan CH, McPherson A, Salehi S, Vázquez-García I, Kabeer F, Lee H, Masud T, Eirew P, Yap D. Evolutionary tracking of cancer haplotypes at single-cell resolution. bioRxiv. 2021. link
Funnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Masud T, Eirew P, Yap D, Zhang AW. The impact of mutational processes on structural genomic plasticity in cancer cells. bioRxiv. 2021 link
Dorri F, Salehi S, Chern K, Funnell T, Williams MJ, Lai D, Andronescu M, Campbell KR, McPherson A, Aparicio S, Roth A. Efficient Bayesian inference of phylogenetic trees from large scale, low-depth genome-wide single-cell data. bioRxiv. 2020 Jan 1.
Cross W, Mossner M, Nowinski S, Cresswell G, Banerjee A, Williams MJ, Gay L, Baker AM, Kimberley C, Davis H, Martinez P. Stabilising selection causes grossly altered but stable karyotypes in metastatic colorectal cancer. bioRxiv. 2020 Jan 1.
Peer reviewed articles
Williams MJ, Zapata L, Werner B, Barnes C, Sottoriva A, Graham TA. Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios. eLife 2020 link
Williams MJ, Werner B, Heide T, Curtis C, Barnes CP, Sottoriva A, Graham TA. Quantification of subclonal selection in cancer from bulk sequencing data. Nature genetics. 2018 Jun;50(6):895-903. http://doi.org/10.1038/s41588-018-0128-6 PDF preprint)
Details of some of the software I developed to implement the ideas in this paper are available here.
- Williams MJ, Werner B, Barnes CP, Graham TA, Sottoriva A. Identification of neutral tumor evolution across cancer types. Nature genetics. 2016 Mar;48(3):238-44.. http://doi.org/10.1038/ng.3489 PDF
This paper generated quite a lot of debate. There are various letters and replies in a number of journals and preprint servers. Andrea Sottoriva has been keeping an updated list of all these which you can find here.
Reviews and commentaries
Williams MJ, Sottoriva A, Graham TA. Measuring clonal evolution in cancer with genomics. Annual review of genomics and human genetics. 2019 Aug 31;20:309-29. link
Williams MJ, Werner B, Graham TA, Sottoriva A. Functional versus non-functional intratumor heterogeneity in cancer. Molecular & cellular oncology. 2016 Jul 3;3(4):e1162897.
Other articles I contributed to
Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D. Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Nature. 2021 Jun 23:1-6. link
Sequeira I, Rashid M, Tomás IM, Williams MJ, Graham TA, Adams DJ, Vigilante A, Watt FM. Genomic landscape and clonal architecture of mouse oral squamous cell carcinomas dictate tumour ecology. Nature communications. 2020 Nov 9;11(1):1-3.
Lakatos E, Williams MJ, Schenck RO, Cross WC, Househam J, Zapata L, Werner B, Gatenbee C, Robertson-Tessi M, Barnes CP, Anderson AR. Evolutionary dynamics of neoantigens in growing tumors. Nature genetics. 2020 Oct;52(10):1057-66. link
Measuring single cell divisions in human cancers from multi-region sequencing data. Werner B.§, Case J., Williams M.J., Chkhaidze K., Temko D., Fernandez-Mateos J., Cresswell G.D., Nichol D., Cross W., Spiteri I., Huang W., Tomlinson I., Barnes C.P., Graham T.A.§, Sottoriva A.§. Nature Communications, 2020 link
Caravagna G, Heide T, Williams MJ, Zapata L, Nichol D, Chkhaidze K, Cross W, Cresswell GD, Werner B, Acar A, Chesler L. Subclonal reconstruction of tumors by using machine learning and population genetics. Nature genetics. 2020 Sep;52(9):898-907. link
Rashid S, Freitas MO, Cucchi D, Bridge G, Yao Z, Gay L, Williams MJ, Wang J, Suraweera N, Silver A, McDonald SA. MLH1 deficiency leads to deregulated mitochondrial metabolism. Cell death & disease. 2019 Oct 22;10(11):1-1.
Chkhaidze K, Heide T, Werner B, Williams MJ, Huang W, Caravagna G, Graham TA, Sottoriva A. Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. PLoS computational biology. 2019 Jul 29;15(7):e1007243. link
Baker AM, Gabbutt C, Williams MJ, Cereser B, Jawad N, Rodriguez-Justo M, Jansen M, Barnes CP, Simons BD, McDonald SA, Graham TA. Crypt fusion as a homeostatic mechanism in the human colon. Gut. 2019 Nov 1;68(11):1986-93. link
Temko D, van Gool IC, Rayner E, Glaire M, Makino S, Brown M, Chegwidden L, Palles C, Depreeuw J, Beggs A, Stathopoulou C, Mason J, Baker A-M, Williams, M, Cerundolo V, Rei M, Taylor JC, Schuh A, Ahmed A, Amant F, Lambrechts D, Smit VT, Bosse T, Graham TA, Church DN, Tomlinson I. Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response. The Journal of Pathology. 2018 Jul;245(3):283–96. link
Baker A-M, Cross W, Curtius K, Bakir Al I, Choi C-HR, Davis HL, Temko D, Biswas S, Martinez P, Williams MJ, Lindsay JO, Feakins R, Vega R, Hayes SJ, Tomlinson IPM, McDonald SAC, Moorghen M, Silver A, East JE, Wright NA, Wang LM, Rodriguez-Justo M, Jansen M, Hart AL, Leedham SJ, Graham TA. Evolutionary history of human colitis-associated colorectal cancer. Gut. 2018 Jul 10 link